Hostname: page-component-cd9895bd7-jkksz Total loading time: 0 Render date: 2024-12-30T14:40:34.989Z Has data issue: false hasContentIssue false
  • English
  • Français

Genetic diversity of farmer-preferred cassava landraces in Tanzania based on morphological descriptors and single nucleotide polymorphisms

Published online by Cambridge University Press:  03 November 2015

M. K. Mtunguja ,
A. Ranjan ,
H. S. Laswai ,
Y. Muzanila ,
J. Ndunguru  and
N. R. Sinha
M. K. Mtunguja*
Affiliation:
Department of Food Science and Technology, Faculty of Agriculture, Sokoine University of Agriculture, P.O. Box 3006, Morogoro, Tanzania Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA95616, USA
A. Ranjan
Affiliation:
Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA95616, USA National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi110067, India
H. S. Laswai
Affiliation:
Department of Food Science and Technology, Faculty of Agriculture, Sokoine University of Agriculture, P.O. Box 3006, Morogoro, Tanzania
Y. Muzanila
Affiliation:
Department of Biological Science, Faculty of Science, Sokoine University of Agriculture, P.O. Box 3038, Morogoro, Tanzania
J. Ndunguru
Affiliation:
Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
N. R. Sinha
Affiliation:
Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA95616, USA
*
*Corresponding author. E-mail: mkmtunguja@gmail.com
Get access Rights & Permissions [Opens in a new window]

Abstract

Cassava germplasm collection is important for the preservation of genetic variability, allowing the development of improved cultivars with desirable traits such as drought and disease tolerance, better starch quality and yield. Therefore, the assessment of diversity in cassava germplasm maintained by farmers is important for maintaining biodiversity and crop improvement. Herein, we report genetic diversity relationships of 52 farmer-preferred cassava landraces from the eastern zone of Tanzania based on morphological descriptors and single nucleotide polymorphisms (SNPs). Cluster analysis was performed for both morphological traits (genetic distance 1.18–0.15) and SNPs (genetic distance 0.078–0.002). The analysis revealed that there were a total of 17,393 variant positions, and that several of the SNPs were distributed across all the chromosomes. The abundance of SNP varied remarkably among the 18 cassava chromosomes, with chromosome 2 having the highest number of SNPs (1335) and chromosome 18 having the lowest number of SNPs (734). The power of SNPs in distinguishing morphologically similar landraces was shown. Both analyses did not group landraces according to geographical locations, suggesting that farmers were moving cassava germplasm to different areas. Their diversity was mainly due to adaptation and preferential selection by farmers. This further implied that within a geographical location, the cultivars were more diverse and there was no misnaming of cassava cultivars by farmers. The collection revealed a wide range of genetic diversity, and represented a valuable resource for trait improvement, allowing the capture of farmer-preferred traits in future cassava breeding programmes.

Keywords

genetic diversitygenetic resourcesgenotype-by-sequencingManihot esculentanext-generation sequencingSNPs
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 2 , April 2017 , pp. 138 - 146
Copyright
Copyright © NIAB 2015 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Benesi, IRM, Lubuschagne, MT and Mahungu, N (2010) Ethnobotany, morphology and genotyping of cassava germplasm from Malawi. Journal of Biological Sciences 10: 616–623.Google Scholar
Ching, A, Caldwell, KS, Jung, M, Dolan, M, Smith, OS, Tingey, S, Morgante, M and Rafalski, AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3: 1–14.Google Scholar
Dellaporta, SL, Wood, J and Hicks, JB (1983) A plant DNA minipreparation: Version 2. Plant Molecular Biology Reporter 1: 19–22.CrossRefGoogle Scholar
Elias, M, Penet, L, Vindry, P, MacKey, D, Panaud, O and Robert, T (2001) Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system. Molecular Ecology 10: 1895–1907.Google Scholar
FAO Report (2006) Starch market adds value to cassava. Available at: http://www.fao.org/ag/magazine/0610sp1.htm (accessed accessed 10 March 2015).Google Scholar
Fukuda, WMG, Guevara, CL, Kawuki, R and Ferguson, ME (2010) Selected Morphological and Agronomic Descriptors for the Characterization of Cassava. Ibadan, Nigeria: International Institute of Tropical Agriculture (IITA).Google Scholar
Garcia-Lor, A, Curk, F, Snoussi-Trifa, H, Morillon, R, Ancillo, G, Luro, F, Navarro, L and Ollitraut, P (2013) A nuclear phylogenetic analysis; SNPs, indels and SSRs deliver new insight into relationship in the ‘true citrus fruit tree’ group (Citranae, Rutaceae) and the origin of cultivated species. Annals of Botany 111: 1–19.Google Scholar
Glaubitz, JC, Cassteve, TM, Lu, F, Harriman, J, Elshire, RJ, Sun, Q and Buckler, ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLOS ONE 9: e90346.Google Scholar
Hershey, CH (1993) Manihot esculenta Crantz. In: Kalloo G and Berg BO (eds) Genetic Improvement of Vegetable Crops. New York: Pergamon press, pp. 669–691. Google Scholar
Kawuki, RS, Ferguson, M, Labuschagne, M, Herseliman, L and Kim, D (2009) Identification, characterisation and application of single nucleotide polymorphisms for diversity assessment in cassava (Manihot esculenta Crantz). Molecular Breeding 23: 669–684.Google Scholar
Kizito, EB, Chiwona-Karltun, L, Egwang, T, Fregene, M and Westerbergh, A (2007) Genetic diversity and variety composition of cassava on small scale farms in Uganda: an interdisciplinary study using genetic markers and farmer interviews. Genetica 130: 301–318.Google Scholar
Lebot, V (2009) Tropical Root and Tuber Crops: Cassava, Sweet Potato, Yams and Aroids. Wallingford, UK: CABI.Google Scholar
Mammadov, J, Aggarwal, R, Buyyarapu, R and Kumpatla, S (2012) SNP markers and their impact on plant breeding. International Journal of Plant Genomics 2012: 1–11.Google Scholar
Mezette, FT, Blumer, GC and Veasey, EA (2013) Morphological and molecular diversity among cassava genotypes. Pesquisa Agropecuária Brasileira 48: 510–518.Google Scholar
Mkamilo, GS and Jeremiah, SC (2005) Current status of cassava improvement program in Tanzania. African Crop Science Conference Proceedings 7: 1311–1314.Google Scholar
Mkumbira, J, Chiwona-Karltun, L, Lagercrantz, U, Mahungu, MN, Saka, J, Mhone, A, Bokanga, M, Brimer, L, Gullberg, U and Rosling, H (2003) Classifications of cassava into bitter and cool: from farmers' perception to characterization by molecular markers. Euphytica 132: 7–22.CrossRefGoogle Scholar
Monson-Miller, J, Sanches-Mendez, DC, Fass, J, Henry, IM, Tai, TH and Comal, L (2012) Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. BioMed Central Genomics 13: 72.Google Scholar
Mtunguja, MK, Laswai, HS, Muzanila, YC and Ndunguru, J (2014) Farmer's knowledge on selection and conservation of cassava (Manihot esculenta) genetic resources in Tanzania. Journal of Biology, Agriculture and Healthcare 4: 120–129.Google Scholar
Oliveira, EJ, Ferreira, CF, Silva Santos, V, de Juses, ON, Oliveira, GAF and Silva, MS (2014) Potential of SNP markers for the characterization of Brazilian cassava germplasm. Theoretical and Applied Genetics 127: 1423–1440.CrossRefGoogle ScholarPubMed
Pujol, B, Renoux, F, Elias, M, Rival, L and Mckey, D (2007) The unappreciated ecology of landrace populations: conservation consequences of soil seed banks in cassava. Biological Conservation 136: 541–551.CrossRefGoogle Scholar
Rafalski, JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant science 162: 329–333.Google Scholar
Raji, AA, Dixon, AGO and Ladeinde, TAO (2007) Agronomic traits and tuber quality attributes of farmer grown cassava (Manihot esculenta) landraces in Nigeria. Journal of Tropical Agriculture 45: 9–13.Google Scholar
Raman, H, Stodart, BJ, Cavanagh, C, Mackay, M, Matthew, M, Milgate, A and Martin, P (2010) Molecular diversity and genetic structure of modern and traditional landrace cultivars of wheat (Triticum aestivum L.). Crop and Pasture Science 61: 222–229.Google Scholar
Rohlf, FJ (2009) NTSYSpc: Numerical Taxonomy System. Ver. 2.21c. Setauket, NY: Exeter Software.Google Scholar
Tairo, F, Mneney, E and Kullaya, A (2008) Morphological and agronomical characterization of sweetpotato [Ipomoea batatas (L.) Lam.] germplasm collection from Tanzania. African Journal of Plant Science 2: 77–85.Google Scholar
Varshney, RK, Nayak, SN, May, GD and Jackson, SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trend in Biotechnology 27: 522–530.Google Scholar
Vieira, EA, Carvalho, FIF, Bertan, I, Kopp, MM, Zimmer, PD, Benin, G, Silva, JAG, Hartwig, I, Malone, G and Oliveira, AC (2007) Association between genetic distances in wheat (Triticum aestivum L.) as estimated by AFLP and morphological markers. Genetics and Molecular Biology 30: 392–399.CrossRefGoogle Scholar
Supplementary material: File

Mtunguja supplementary material

Table S1 and Figures S1-S2

Download Mtunguja supplementary material(File)
File 81.4 KB